[Chimera-users] the fastest way to convert a pdb to density map

Tom Goddard goddard at sonic.net
Fri Jan 22 11:19:18 PST 2016

Hi Zhihai,

Yes use molmap then vop resample.  If your atomic model is #0 and experimental map is #1 with resolution 5 Angstroms use

	molmap #0 5
	vop resample #2 ongrid #1

For computing FSC it should not matter what resolution you use with molmap because that resolution value will just scale the Fourier shells and should not alter the correlation with a shell.  But I would test to make sure this is the case.  Also if you are at very high resolution (3 - 4 Angstroms) I am not sure the molmap map is good enough an approximation since it simply puts a Gaussian at each atom position with all Gaussians having the same standard deviation.


> On Jan 22, 2016, at 5:25 AM, 李智海 < wrote:
> Maybe now I find the answer to my own question, the command combinations molmap onGrid and vop resample can solve my problem.
> Zhihai
>> On Jan 22, 2016, at 9:00 PM, 李智海  wrote:
>> Hi,
>> Here I want to calculate a model-to-map FSC curve. If I am not wrong, firstly I am supposed to convert the pdb file to a density map. So I was just wondering in Chimera, how to use command molmap to generated a map with the same pixel size and dimensions as the corresponding map?
>> Any help will be high appreciated.
>> Best,
>> Zhihai Li
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